I think you can put the flannel and cotton together in a quilt without too much problem but...I would make sure that I washed both first and also put them in the dryer. I usually do this on a hotter temperature, not cold. I want the fabrics to get their shrinking over with before cutting and stitching. Flannel almost always shrinks way more than cotton although I have had some cotton quilting fabric shrink a fair amount also. This will also remove excess chemicals used in production from the fabric for the baby. I am not sure of the lining for maybe the wedding dresses as I wouldn't have any idea of the content of that. I think I would put that aside for someother use.